# Generated by roxygen2: do not edit by hand

S3method("[",DBS136Catalog)
S3method("[",DBS144Catalog)
S3method("[",DBS78Catalog)
S3method("[",ID166Catalog)
S3method("[",IndelCatalog)
S3method("[",SBS1536Catalog)
S3method("[",SBS192Catalog)
S3method("[",SBS96Catalog)
S3method(PlotCatalog,DBS136Catalog)
S3method(PlotCatalog,DBS144Catalog)
S3method(PlotCatalog,DBS78Catalog)
S3method(PlotCatalog,ID166Catalog)
S3method(PlotCatalog,IndelCatalog)
S3method(PlotCatalog,SBS1536Catalog)
S3method(PlotCatalog,SBS192Catalog)
S3method(PlotCatalog,SBS96Catalog)
S3method(PlotCatalogToPdf,DBS136Catalog)
S3method(PlotCatalogToPdf,DBS144Catalog)
S3method(PlotCatalogToPdf,DBS78Catalog)
S3method(PlotCatalogToPdf,ID166Catalog)
S3method(PlotCatalogToPdf,IndelCatalog)
S3method(PlotCatalogToPdf,SBS1536Catalog)
S3method(PlotCatalogToPdf,SBS192Catalog)
S3method(PlotCatalogToPdf,SBS96Catalog)
S3method(WriteCatalog,COMPOSITECatalog)
S3method(WriteCatalog,DBS136Catalog)
S3method(WriteCatalog,DBS144Catalog)
S3method(WriteCatalog,DBS78Catalog)
S3method(WriteCatalog,ID166Catalog)
S3method(WriteCatalog,IndelCatalog)
S3method(WriteCatalog,SBS1536Catalog)
S3method(WriteCatalog,SBS192Catalog)
S3method(WriteCatalog,SBS96Catalog)
S3method(cbind,DBS136Catalog)
S3method(cbind,DBS144Catalog)
S3method(cbind,DBS78Catalog)
S3method(cbind,ID166Catalog)
S3method(cbind,IndelCatalog)
S3method(cbind,SBS1536Catalog)
S3method(cbind,SBS192Catalog)
S3method(cbind,SBS96Catalog)
export(AnnotateDBSVCF)
export(AnnotateIDVCF)
export(AnnotateSBSVCF)
export(Canonicalize1Del)
export(Collapse144CatalogTo78)
export(Collapse1536CatalogTo96)
export(Collapse192CatalogTo96)
export(ConvertCatalogToSigProfilerFormat)
export(FindDelMH)
export(FindMaxRepeatDel)
export(GetFreebayesVAF)
export(GetMutectVAF)
export(GetPCAWGConsensusVAF)
export(GetStrelkaVAF)
export(IsICAMSCatalog)
export(MutectVCFFilesToCatalog)
export(MutectVCFFilesToCatalogAndPlotToPdf)
export(MutectVCFFilesToZipFile)
export(PlotCatalog)
export(PlotCatalogToPdf)
export(PlotTransBiasGeneExp)
export(PlotTransBiasGeneExpToPdf)
export(ReadAndSplitMutectVCFs)
export(ReadAndSplitStrelkaSBSVCFs)
export(ReadAndSplitVCFs)
export(ReadCatalog)
export(ReadStrelkaIDVCFs)
export(ReadVCFs)
export(SimpleReadVCF)
export(SplitListOfVCFs)
export(StrelkaIDVCFFilesToCatalog)
export(StrelkaIDVCFFilesToCatalogAndPlotToPdf)
export(StrelkaIDVCFFilesToZipFile)
export(StrelkaSBSVCFFilesToCatalog)
export(StrelkaSBSVCFFilesToCatalogAndPlotToPdf)
export(StrelkaSBSVCFFilesToZipFile)
export(TransformCatalog)
export(VCFsToCatalogs)
export(VCFsToCatalogsAndPlotToPdf)
export(VCFsToDBSCatalogs)
export(VCFsToIDCatalogs)
export(VCFsToSBSCatalogs)
export(VCFsToZipFile)
export(WriteCatalog)
export(as.catalog)
export(revc)
import(data.table)
import(graphics)
importFrom(BSgenome,getSeq)
importFrom(BSgenome,seqnames)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,reduce)
importFrom(IRanges,IRanges)
importFrom(data.table,as.data.table)
importFrom(dplyr,"%>%")
importFrom(dplyr,bind_rows)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,summarize)
importFrom(parallel,mclapply)
importFrom(stats,binom.test)
importFrom(stats,end)
importFrom(stats,glm)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,start)
importFrom(stringi,stri_pad)
importFrom(stringi,stri_split_fixed)
importFrom(tools,md5sum)
importFrom(utils,glob2rx)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(zip,zipr)
